Starting phenix.real_space_refine on Wed May 28 10:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uhw_42284/05_2025/8uhw_42284_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uhw_42284/05_2025/8uhw_42284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uhw_42284/05_2025/8uhw_42284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uhw_42284/05_2025/8uhw_42284.map" model { file = "/net/cci-nas-00/data/ceres_data/8uhw_42284/05_2025/8uhw_42284_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uhw_42284/05_2025/8uhw_42284_neut.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 5 7.16 5 S 204 5.16 5 C 19632 2.51 5 N 5096 2.21 5 O 5851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 1.53s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30788 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2035 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 13, 'TRANS': 251} Chain breaks: 5 Chain: "B" Number of atoms: 6626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6626 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 37, 'TRANS': 821} Chain: "C" Number of atoms: 6626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6626 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 37, 'TRANS': 821} Chain: "D" Number of atoms: 6626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6626 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 37, 'TRANS': 821} Chain: "E" Number of atoms: 6626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6626 Classifications: {'peptide': 859} Link IDs: {'PTRANS': 37, 'TRANS': 821} Chain: "F" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2244 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 14, 'TRANS': 278} Chain breaks: 4 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.06, per 1000 atoms: 0.65 Number of scatterers: 30788 At special positions: 0 Unit cell: (158.26, 196.8, 127.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 5 26.01 S 204 16.00 O 5851 8.00 N 5096 7.00 C 19632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.95 Conformation dependent library (CDL) restraints added in 4.4 seconds 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7454 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 23 sheets defined 57.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 472 through 485 removed outlier: 4.298A pdb=" N LEU A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 503 through 513 removed outlier: 3.677A pdb=" N MET A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 543 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.753A pdb=" N MET A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 671 Processing helix chain 'A' and resid 675 through 700 removed outlier: 3.702A pdb=" N GLU A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 703 through 724 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 797 through 814 removed outlier: 3.804A pdb=" N GLU A 801 " --> pdb=" O GLU A 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 32 Processing helix chain 'B' and resid 35 through 53 Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.970A pdb=" N LEU B 57 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 88 removed outlier: 4.376A pdb=" N ILE B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 139 removed outlier: 3.808A pdb=" N THR B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 167 removed outlier: 4.241A pdb=" N ALA B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 264 through 275 removed outlier: 3.658A pdb=" N ARG B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.587A pdb=" N ILE B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.676A pdb=" N HIS B 340 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 369 removed outlier: 3.550A pdb=" N ASP B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 393 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.105A pdb=" N ILE B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 441 through 445 removed outlier: 4.006A pdb=" N LEU B 445 " --> pdb=" O LYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.690A pdb=" N LEU B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.031A pdb=" N MET B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 543 Processing helix chain 'B' and resid 553 through 568 removed outlier: 4.077A pdb=" N ASP B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.795A pdb=" N ARG B 586 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.528A pdb=" N VAL B 612 " --> pdb=" O GLY B 609 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 613 " --> pdb=" O SER B 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 609 through 613' Processing helix chain 'B' and resid 632 through 635 Processing helix chain 'B' and resid 642 through 647 removed outlier: 3.841A pdb=" N MET B 645 " --> pdb=" O ASP B 642 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET B 647 " --> pdb=" O ASP B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 671 Processing helix chain 'B' and resid 675 through 699 Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 703 through 724 Processing helix chain 'B' and resid 727 through 741 removed outlier: 3.671A pdb=" N SER B 731 " --> pdb=" O GLY B 727 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS B 735 " --> pdb=" O SER B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 750 Processing helix chain 'B' and resid 751 through 760 removed outlier: 3.831A pdb=" N ARG B 757 " --> pdb=" O ASN B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 790 Processing helix chain 'B' and resid 797 through 814 Processing helix chain 'B' and resid 820 through 824 Processing helix chain 'B' and resid 826 through 843 removed outlier: 4.408A pdb=" N ASP B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU B 836 " --> pdb=" O ASP B 832 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 839 " --> pdb=" O ASP B 835 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN B 840 " --> pdb=" O GLU B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 850 removed outlier: 3.576A pdb=" N GLY B 848 " --> pdb=" O GLN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 869 Processing helix chain 'C' and resid 13 through 32 removed outlier: 3.551A pdb=" N VAL C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.782A pdb=" N LEU C 57 " --> pdb=" O MET C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 88 removed outlier: 4.409A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 150 through 169 removed outlier: 4.170A pdb=" N ALA C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 191 Processing helix chain 'C' and resid 203 through 209 Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 264 through 274 Processing helix chain 'C' and resid 282 through 293 removed outlier: 3.994A pdb=" N GLU C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE C 293 " --> pdb=" O ARG C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 354 through 368 Processing helix chain 'C' and resid 384 through 395 Processing helix chain 'C' and resid 405 through 411 removed outlier: 3.936A pdb=" N ILE C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 removed outlier: 3.525A pdb=" N HIS C 443 " --> pdb=" O GLY C 440 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU C 445 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 478 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'C' and resid 503 through 514 removed outlier: 3.522A pdb=" N LYS C 509 " --> pdb=" O PRO C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 543 removed outlier: 3.721A pdb=" N ALA C 532 " --> pdb=" O SER C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 568 Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.609A pdb=" N MET C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 635 removed outlier: 3.924A pdb=" N LEU C 635 " --> pdb=" O TYR C 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 635' Processing helix chain 'C' and resid 642 through 647 removed outlier: 4.077A pdb=" N MET C 647 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 671 Processing helix chain 'C' and resid 675 through 700 removed outlier: 3.994A pdb=" N SER C 680 " --> pdb=" O ASP C 676 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU C 681 " --> pdb=" O TYR C 677 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 703 through 724 Processing helix chain 'C' and resid 727 through 740 removed outlier: 3.752A pdb=" N SER C 731 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS C 735 " --> pdb=" O SER C 731 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 738 " --> pdb=" O HIS C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 750 Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 777 through 790 removed outlier: 3.649A pdb=" N ARG C 781 " --> pdb=" O ARG C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 814 Processing helix chain 'C' and resid 820 through 824 removed outlier: 3.796A pdb=" N ASP C 824 " --> pdb=" O LYS C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 843 removed outlier: 4.779A pdb=" N ASP C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLU C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 839 " --> pdb=" O ASP C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 850 removed outlier: 3.572A pdb=" N THR C 849 " --> pdb=" O CYS C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 869 Processing helix chain 'D' and resid 13 through 32 removed outlier: 3.526A pdb=" N VAL D 30 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 53 removed outlier: 3.698A pdb=" N MET D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 66 Processing helix chain 'D' and resid 69 through 86 removed outlier: 3.585A pdb=" N SER D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.623A pdb=" N THR D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 150 through 168 removed outlier: 3.769A pdb=" N THR D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 264 through 275 removed outlier: 3.591A pdb=" N ARG D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.661A pdb=" N ILE D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 354 through 369 Processing helix chain 'D' and resid 384 through 395 Processing helix chain 'D' and resid 405 through 411 removed outlier: 4.136A pdb=" N ILE D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 432 removed outlier: 3.687A pdb=" N GLY D 431 " --> pdb=" O CYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 445 removed outlier: 3.634A pdb=" N HIS D 443 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU D 445 " --> pdb=" O LYS D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.856A pdb=" N GLU D 479 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN D 482 " --> pdb=" O ASP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 500 removed outlier: 3.573A pdb=" N ASN D 500 " --> pdb=" O PHE D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 528 through 543 removed outlier: 3.537A pdb=" N ALA D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 Processing helix chain 'D' and resid 572 through 577 removed outlier: 3.718A pdb=" N MET D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 635 removed outlier: 3.806A pdb=" N LEU D 635 " --> pdb=" O TYR D 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 632 through 635' Processing helix chain 'D' and resid 650 through 670 Processing helix chain 'D' and resid 675 through 699 removed outlier: 3.729A pdb=" N LEU D 681 " --> pdb=" O TYR D 677 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 703 through 724 removed outlier: 3.556A pdb=" N ARG D 707 " --> pdb=" O ASP D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 741 removed outlier: 4.116A pdb=" N SER D 731 " --> pdb=" O GLY D 727 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS D 735 " --> pdb=" O SER D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 750 Processing helix chain 'D' and resid 751 through 760 Processing helix chain 'D' and resid 777 through 790 Processing helix chain 'D' and resid 797 through 814 Processing helix chain 'D' and resid 819 through 824 Processing helix chain 'D' and resid 826 through 843 removed outlier: 5.068A pdb=" N ASP D 835 " --> pdb=" O LEU D 831 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU D 836 " --> pdb=" O ASP D 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 850 removed outlier: 3.592A pdb=" N GLY D 848 " --> pdb=" O GLN D 845 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR D 849 " --> pdb=" O CYS D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 869 Processing helix chain 'E' and resid 13 through 32 removed outlier: 3.504A pdb=" N VAL E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 52 Processing helix chain 'E' and resid 53 through 66 removed outlier: 3.792A pdb=" N LEU E 57 " --> pdb=" O MET E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 89 removed outlier: 4.572A pdb=" N ILE E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.521A pdb=" N THR E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 168 removed outlier: 3.848A pdb=" N THR E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.511A pdb=" N GLU E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 210 Processing helix chain 'E' and resid 232 through 246 Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 264 through 275 Processing helix chain 'E' and resid 281 through 292 Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 354 through 367 Processing helix chain 'E' and resid 384 through 395 removed outlier: 3.637A pdb=" N LEU E 388 " --> pdb=" O GLN E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 472 through 478 Processing helix chain 'E' and resid 494 through 500 Processing helix chain 'E' and resid 503 through 513 removed outlier: 3.615A pdb=" N LYS E 509 " --> pdb=" O PRO E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 552 through 568 Processing helix chain 'E' and resid 572 through 577 Processing helix chain 'E' and resid 582 through 586 removed outlier: 3.781A pdb=" N ARG E 586 " --> pdb=" O ILE E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 613 removed outlier: 4.133A pdb=" N VAL E 612 " --> pdb=" O GLY E 609 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR E 613 " --> pdb=" O SER E 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 609 through 613' Processing helix chain 'E' and resid 631 through 635 removed outlier: 4.019A pdb=" N LEU E 635 " --> pdb=" O TYR E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 646 removed outlier: 3.654A pdb=" N MET E 645 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 671 Processing helix chain 'E' and resid 675 through 700 removed outlier: 4.032A pdb=" N SER E 680 " --> pdb=" O ASP E 676 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU E 681 " --> pdb=" O TYR E 677 " (cutoff:3.500A) Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 703 through 724 removed outlier: 3.542A pdb=" N ARG E 707 " --> pdb=" O ASP E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 727 through 741 removed outlier: 3.830A pdb=" N SER E 731 " --> pdb=" O GLY E 727 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS E 735 " --> pdb=" O SER E 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 750 Processing helix chain 'E' and resid 751 through 760 Processing helix chain 'E' and resid 777 through 790 Processing helix chain 'E' and resid 797 through 814 Processing helix chain 'E' and resid 819 through 824 Processing helix chain 'E' and resid 826 through 843 removed outlier: 4.707A pdb=" N ASP E 835 " --> pdb=" O LEU E 831 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU E 836 " --> pdb=" O ASP E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 845 through 850 removed outlier: 3.652A pdb=" N THR E 849 " --> pdb=" O CYS E 846 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN E 850 " --> pdb=" O THR E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 855 through 869 Processing helix chain 'F' and resid 471 through 478 removed outlier: 4.564A pdb=" N VAL F 475 " --> pdb=" O GLY F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 481 No H-bonds generated for 'chain 'F' and resid 479 through 481' Processing helix chain 'F' and resid 494 through 501 removed outlier: 3.546A pdb=" N ASN F 500 " --> pdb=" O PHE F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 513 removed outlier: 3.584A pdb=" N MET F 513 " --> pdb=" O LYS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 543 removed outlier: 3.625A pdb=" N ALA F 532 " --> pdb=" O SER F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 568 Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 650 through 671 Processing helix chain 'F' and resid 675 through 700 removed outlier: 3.581A pdb=" N LEU F 681 " --> pdb=" O TYR F 677 " (cutoff:3.500A) Proline residue: F 694 - end of helix Processing helix chain 'F' and resid 703 through 724 Processing helix chain 'F' and resid 744 through 750 Processing helix chain 'F' and resid 751 through 760 Processing helix chain 'F' and resid 778 through 790 Processing helix chain 'F' and resid 797 through 815 removed outlier: 3.823A pdb=" N GLU F 801 " --> pdb=" O GLU F 797 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 516 through 520 removed outlier: 6.493A pdb=" N ALA A 489 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE A 520 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 491 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS A 488 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE A 548 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE A 490 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 550 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL A 492 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 547 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE A 602 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A 549 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE A 599 " --> pdb=" O MET A 638 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE A 640 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA A 601 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS A 465 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL A 641 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR A 467 " --> pdb=" O VAL A 641 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.720A pdb=" N ASP B 100 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 105 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER C 375 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR C 378 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 226 " --> pdb=" O TYR C 378 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL C 258 " --> pdb=" O TYR C 350 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA C 352 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 260 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU C 325 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N MET C 349 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY C 327 " --> pdb=" O MET C 349 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ARG C 351 " --> pdb=" O GLY C 327 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU C 328 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.324A pdb=" N ILE B 142 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 195 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 196 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 277 through 279 removed outlier: 5.999A pdb=" N LEU B 325 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N MET B 349 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B 327 " --> pdb=" O MET B 349 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ARG B 351 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 258 " --> pdb=" O TYR B 350 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ALA B 352 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B 260 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 225 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU B 261 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE B 227 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR B 378 " --> pdb=" O PRO B 224 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 226 " --> pdb=" O TYR B 378 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER B 375 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 106 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE C 105 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 466 through 468 Processing sheet with id=AA6, first strand: chain 'B' and resid 516 through 520 removed outlier: 6.402A pdb=" N ALA B 489 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE B 520 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 491 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 615 through 619 Processing sheet with id=AA8, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.378A pdb=" N ILE C 142 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 195 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE C 196 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 459 through 460 removed outlier: 3.646A pdb=" N ILE D 466 " --> pdb=" O PHE C 460 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR D 467 " --> pdb=" O VAL D 641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 466 through 468 removed outlier: 3.836A pdb=" N ILE C 466 " --> pdb=" O PHE D 460 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 458 " --> pdb=" O ILE C 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 516 through 523 removed outlier: 6.498A pdb=" N ALA C 489 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N PHE C 520 " --> pdb=" O ALA C 489 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE C 491 " --> pdb=" O PHE C 520 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASP C 522 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR C 493 " --> pdb=" O ASP C 522 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS C 488 " --> pdb=" O THR C 546 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE C 548 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE C 490 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL C 550 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL C 492 " --> pdb=" O VAL C 550 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 615 through 619 removed outlier: 3.781A pdb=" N ILE C 618 " --> pdb=" O TYR C 627 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 98 through 99 removed outlier: 4.266A pdb=" N GLU D 98 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR D 449 " --> pdb=" O ILE E 400 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL E 402 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA D 451 " --> pdb=" O VAL E 402 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER E 375 " --> pdb=" O LEU E 401 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N TYR E 378 " --> pdb=" O PRO E 224 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 226 " --> pdb=" O TYR E 378 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA E 225 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU E 261 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE E 227 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL E 258 " --> pdb=" O TYR E 350 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALA E 352 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL E 260 " --> pdb=" O ALA E 352 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU E 325 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET E 349 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY E 327 " --> pdb=" O MET E 349 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ARG E 351 " --> pdb=" O GLY E 327 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR E 278 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU E 328 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU E 280 " --> pdb=" O GLU E 328 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 175 through 177 removed outlier: 6.403A pdb=" N ILE D 142 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE D 196 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 277 through 279 removed outlier: 6.443A pdb=" N TYR D 278 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLU D 328 " --> pdb=" O TYR D 278 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU D 325 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N MET D 349 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY D 327 " --> pdb=" O MET D 349 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ARG D 351 " --> pdb=" O GLY D 327 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N TYR D 378 " --> pdb=" O PRO D 224 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE D 226 " --> pdb=" O TYR D 378 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER D 375 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 400 " --> pdb=" O ALA E 451 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS E 107 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 516 through 523 removed outlier: 6.411A pdb=" N ALA D 489 " --> pdb=" O LYS D 518 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE D 520 " --> pdb=" O ALA D 489 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE D 491 " --> pdb=" O PHE D 520 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASP D 522 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR D 493 " --> pdb=" O ASP D 522 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP D 494 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE D 547 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE D 602 " --> pdb=" O ILE D 547 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA D 549 " --> pdb=" O ILE D 602 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 615 through 619 removed outlier: 4.028A pdb=" N ILE D 618 " --> pdb=" O TYR D 627 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 175 through 177 removed outlier: 6.350A pdb=" N ILE E 142 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 195 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE E 196 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 293 through 294 Processing sheet with id=AC2, first strand: chain 'E' and resid 458 through 460 removed outlier: 3.623A pdb=" N ILE F 466 " --> pdb=" O PHE E 460 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE F 599 " --> pdb=" O MET F 638 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE F 640 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA F 601 " --> pdb=" O ILE F 640 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 640 through 641 removed outlier: 6.032A pdb=" N TYR E 467 " --> pdb=" O VAL E 641 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 466 " --> pdb=" O PHE F 460 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 516 through 520 Processing sheet with id=AC5, first strand: chain 'E' and resid 618 through 619 1583 hydrogen bonds defined for protein. 4596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.70 Time building geometry restraints manager: 10.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10019 1.34 - 1.46: 6034 1.46 - 1.58: 14934 1.58 - 1.69: 1 1.69 - 1.81: 370 Bond restraints: 31358 Sorted by residual: bond pdb=" N VAL E 366 " pdb=" CA VAL E 366 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.61e+00 bond pdb=" N VAL D 366 " pdb=" CA VAL D 366 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.98e+00 bond pdb=" N LEU D 365 " pdb=" CA LEU D 365 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.80e+00 bond pdb=" N ARG D 364 " pdb=" CA ARG D 364 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.35e+00 bond pdb=" N ASP E 368 " pdb=" CA ASP E 368 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.31e+00 ... (remaining 31353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 41295 1.58 - 3.16: 938 3.16 - 4.74: 128 4.74 - 6.32: 34 6.32 - 7.90: 7 Bond angle restraints: 42402 Sorted by residual: angle pdb=" N ASP C 413 " pdb=" CA ASP C 413 " pdb=" C ASP C 413 " ideal model delta sigma weight residual 114.64 106.74 7.90 1.52e+00 4.33e-01 2.70e+01 angle pdb=" N ASP E 413 " pdb=" CA ASP E 413 " pdb=" C ASP E 413 " ideal model delta sigma weight residual 114.09 106.61 7.48 1.55e+00 4.16e-01 2.33e+01 angle pdb=" C LYS E 794 " pdb=" N ASN E 795 " pdb=" CA ASN E 795 " ideal model delta sigma weight residual 122.08 128.46 -6.38 1.47e+00 4.63e-01 1.88e+01 angle pdb=" N ALA D 87 " pdb=" CA ALA D 87 " pdb=" C ALA D 87 " ideal model delta sigma weight residual 114.75 109.37 5.38 1.26e+00 6.30e-01 1.83e+01 angle pdb=" CA VAL D 366 " pdb=" C VAL D 366 " pdb=" O VAL D 366 " ideal model delta sigma weight residual 121.17 116.98 4.19 1.06e+00 8.90e-01 1.57e+01 ... (remaining 42397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17048 17.95 - 35.90: 1674 35.90 - 53.86: 322 53.86 - 71.81: 51 71.81 - 89.76: 22 Dihedral angle restraints: 19117 sinusoidal: 7528 harmonic: 11589 Sorted by residual: dihedral pdb=" CA GLY D 412 " pdb=" C GLY D 412 " pdb=" N ASP D 413 " pdb=" CA ASP D 413 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA SER D 422 " pdb=" C SER D 422 " pdb=" N LEU D 423 " pdb=" CA LEU D 423 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ILE E 411 " pdb=" C ILE E 411 " pdb=" N GLY E 412 " pdb=" CA GLY E 412 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 19114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3486 0.041 - 0.082: 998 0.082 - 0.124: 303 0.124 - 0.165: 38 0.165 - 0.206: 2 Chirality restraints: 4827 Sorted by residual: chirality pdb=" CA ASP E 368 " pdb=" N ASP E 368 " pdb=" C ASP E 368 " pdb=" CB ASP E 368 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR E 424 " pdb=" CA THR E 424 " pdb=" OG1 THR E 424 " pdb=" CG2 THR E 424 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA ASN E 795 " pdb=" N ASN E 795 " pdb=" C ASN E 795 " pdb=" CB ASN E 795 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 4824 not shown) Planarity restraints: 5446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 473 " 0.063 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO B 474 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 474 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 474 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 201 " -0.048 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO D 202 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 202 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 202 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 110 " 0.038 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO C 111 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " 0.031 5.00e-02 4.00e+02 ... (remaining 5443 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3620 2.75 - 3.29: 29691 3.29 - 3.83: 50013 3.83 - 4.36: 58768 4.36 - 4.90: 104843 Nonbonded interactions: 246935 Sorted by model distance: nonbonded pdb=" NE2 HIS F 744 " pdb="FE FE F 901 " model vdw 2.216 2.340 nonbonded pdb=" OG SER D 243 " pdb=" OE1 GLU D 255 " model vdw 2.223 3.040 nonbonded pdb=" NE2 HIS E 730 " pdb="FE FE E 901 " model vdw 2.235 2.340 nonbonded pdb=" OH TYR E 265 " pdb=" OE1 GLU E 328 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR E 467 " pdb=" OE2 GLU E 479 " model vdw 2.252 3.040 ... (remaining 246930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 458 through 571 or resid 594 through 815)) selection = (chain 'F' and (resid 458 through 523 or resid 526 through 571 or resid 594 thro \ ugh 614 or resid 632 through 725 or resid 778 through 789 or resid 795 through 8 \ 15)) } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.420 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 72.050 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 31358 Z= 0.140 Angle : 0.587 7.904 42402 Z= 0.347 Chirality : 0.042 0.206 4827 Planarity : 0.005 0.093 5446 Dihedral : 14.643 89.761 11663 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.09 % Allowed : 0.21 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3964 helix: 1.45 (0.12), residues: 2100 sheet: -0.48 (0.23), residues: 500 loop : -1.53 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 563 HIS 0.004 0.001 HIS D 734 PHE 0.025 0.001 PHE D 44 TYR 0.010 0.001 TYR C 677 ARG 0.009 0.000 ARG E 191 Details of bonding type rmsd hydrogen bonds : bond 0.15060 ( 1583) hydrogen bonds : angle 5.32730 ( 4596) covalent geometry : bond 0.00271 (31358) covalent geometry : angle 0.58741 (42402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 697 time to evaluate : 3.235 Fit side-chains revert: symmetry clash REVERT: A 499 ASN cc_start: 0.6612 (m-40) cc_final: 0.6235 (m-40) REVERT: A 538 GLU cc_start: 0.7084 (tt0) cc_final: 0.6568 (mt-10) REVERT: A 568 HIS cc_start: 0.6194 (m-70) cc_final: 0.5922 (m90) REVERT: A 571 VAL cc_start: 0.6043 (t) cc_final: 0.5690 (m) REVERT: A 611 GLU cc_start: 0.8227 (pm20) cc_final: 0.7875 (pm20) REVERT: A 645 MET cc_start: 0.8397 (mmm) cc_final: 0.8124 (mmt) REVERT: A 651 LYS cc_start: 0.7088 (mttm) cc_final: 0.6532 (mtpt) REVERT: A 667 GLU cc_start: 0.6438 (mp0) cc_final: 0.6135 (mp0) REVERT: A 809 GLU cc_start: 0.6398 (tt0) cc_final: 0.5783 (mt-10) REVERT: A 813 LYS cc_start: 0.6482 (mttt) cc_final: 0.5957 (mttt) REVERT: B 11 ILE cc_start: 0.7529 (mt) cc_final: 0.7319 (mp) REVERT: B 41 LYS cc_start: 0.7537 (tttt) cc_final: 0.7292 (tttp) REVERT: B 60 MET cc_start: 0.7839 (ttm) cc_final: 0.7500 (ttm) REVERT: B 156 GLU cc_start: 0.7051 (tp30) cc_final: 0.6829 (tp30) REVERT: B 159 LYS cc_start: 0.7421 (mttt) cc_final: 0.7076 (mttt) REVERT: B 160 ILE cc_start: 0.8466 (mm) cc_final: 0.8172 (mt) REVERT: B 222 ASN cc_start: 0.7914 (m-40) cc_final: 0.7535 (m110) REVERT: B 284 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7031 (mt-10) REVERT: B 301 LYS cc_start: 0.7320 (mmpt) cc_final: 0.7115 (mmtm) REVERT: B 312 ASN cc_start: 0.6652 (t0) cc_final: 0.5970 (m-40) REVERT: B 390 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7913 (ttmm) REVERT: B 470 ARG cc_start: 0.6691 (ttt-90) cc_final: 0.6465 (ttt-90) REVERT: B 481 LYS cc_start: 0.6466 (tptm) cc_final: 0.5928 (tppt) REVERT: B 486 LYS cc_start: 0.6462 (mmtt) cc_final: 0.6241 (mmtm) REVERT: B 592 LYS cc_start: 0.7620 (mttm) cc_final: 0.6998 (tptt) REVERT: B 663 THR cc_start: 0.8502 (m) cc_final: 0.8243 (p) REVERT: B 687 LYS cc_start: 0.7838 (tttt) cc_final: 0.7119 (tptp) REVERT: B 692 TYR cc_start: 0.8235 (m-80) cc_final: 0.7797 (m-10) REVERT: B 709 LYS cc_start: 0.6690 (mmtm) cc_final: 0.6455 (mmtp) REVERT: B 736 LEU cc_start: 0.7516 (tp) cc_final: 0.7305 (tp) REVERT: B 740 TYR cc_start: 0.7921 (m-80) cc_final: 0.7582 (m-80) REVERT: B 764 PRO cc_start: 0.8200 (Cg_endo) cc_final: 0.7967 (Cg_exo) REVERT: B 780 GLU cc_start: 0.6876 (mp0) cc_final: 0.6459 (tt0) REVERT: C 16 LYS cc_start: 0.6901 (mmtt) cc_final: 0.6186 (mtmt) REVERT: C 23 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.6858 (ttp80) REVERT: C 160 ILE cc_start: 0.8116 (mm) cc_final: 0.7914 (mm) REVERT: C 186 THR cc_start: 0.8016 (m) cc_final: 0.7762 (p) REVERT: C 191 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7539 (mtp180) REVERT: C 262 ASP cc_start: 0.7398 (m-30) cc_final: 0.6933 (m-30) REVERT: C 353 LYS cc_start: 0.7117 (ptpp) cc_final: 0.6371 (mmtm) REVERT: C 363 GLU cc_start: 0.6577 (tt0) cc_final: 0.6275 (mt-10) REVERT: C 364 ARG cc_start: 0.6640 (tpt-90) cc_final: 0.5567 (tpp-160) REVERT: C 385 LYS cc_start: 0.7439 (mmtp) cc_final: 0.6693 (mmmt) REVERT: C 470 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7563 (mtp180) REVERT: C 567 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7965 (mt-10) REVERT: C 625 ILE cc_start: 0.8213 (mt) cc_final: 0.7865 (pt) REVERT: C 627 TYR cc_start: 0.5926 (m-80) cc_final: 0.5653 (m-80) REVERT: C 645 MET cc_start: 0.8527 (mmm) cc_final: 0.8319 (mmm) REVERT: C 648 ASN cc_start: 0.8722 (m110) cc_final: 0.8499 (m-40) REVERT: D 100 ASP cc_start: 0.7144 (t0) cc_final: 0.6849 (t0) REVERT: D 149 ARG cc_start: 0.8059 (ttm170) cc_final: 0.7780 (ttm170) REVERT: D 228 ASP cc_start: 0.7645 (p0) cc_final: 0.7409 (p0) REVERT: D 269 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7536 (ttmt) REVERT: D 356 ASP cc_start: 0.6618 (m-30) cc_final: 0.6323 (m-30) REVERT: D 386 GLU cc_start: 0.6711 (pp20) cc_final: 0.6424 (pp20) REVERT: D 436 SER cc_start: 0.8648 (t) cc_final: 0.8262 (p) REVERT: D 496 PHE cc_start: 0.8022 (t80) cc_final: 0.7803 (t80) REVERT: D 565 MET cc_start: 0.7622 (mtp) cc_final: 0.7396 (mtp) REVERT: D 574 MET cc_start: 0.7079 (mmt) cc_final: 0.6801 (tpt) REVERT: D 626 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7883 (mtmm) REVERT: D 828 LYS cc_start: 0.7357 (ttpp) cc_final: 0.6926 (ttpt) REVERT: D 843 ASP cc_start: 0.7605 (t0) cc_final: 0.7112 (t70) REVERT: E 152 ASN cc_start: 0.7152 (m-40) cc_final: 0.5983 (m110) REVERT: E 159 LYS cc_start: 0.7674 (mttt) cc_final: 0.7322 (mttt) REVERT: E 181 PRO cc_start: 0.8335 (Cg_endo) cc_final: 0.7987 (Cg_exo) REVERT: E 192 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6859 (mm-30) REVERT: E 356 ASP cc_start: 0.7346 (m-30) cc_final: 0.6780 (m-30) REVERT: E 465 LYS cc_start: 0.7443 (mttm) cc_final: 0.7177 (mttm) REVERT: E 470 ARG cc_start: 0.6687 (mtp-110) cc_final: 0.6117 (ttm170) REVERT: E 480 LEU cc_start: 0.6529 (mp) cc_final: 0.6271 (mt) REVERT: E 481 LYS cc_start: 0.5481 (ptmt) cc_final: 0.5271 (pptt) REVERT: E 576 MET cc_start: 0.8131 (mtm) cc_final: 0.7894 (mtm) REVERT: E 757 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.6960 (mtt-85) REVERT: F 533 LYS cc_start: 0.6671 (mmtp) cc_final: 0.6346 (mmmt) REVERT: F 751 MET cc_start: 0.6296 (mtp) cc_final: 0.5477 (mtm) REVERT: F 780 GLU cc_start: 0.6712 (pm20) cc_final: 0.6207 (pt0) REVERT: F 787 ASP cc_start: 0.6429 (t0) cc_final: 0.6082 (t0) REVERT: F 802 ASN cc_start: 0.5660 (m-40) cc_final: 0.5428 (m-40) outliers start: 3 outliers final: 0 residues processed: 699 average time/residue: 0.4121 time to fit residues: 454.7540 Evaluate side-chains 541 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 358 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 384 GLN E 865 ASN F 664 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.144582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.117875 restraints weight = 35685.102| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.62 r_work: 0.3008 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31358 Z= 0.169 Angle : 0.578 7.264 42402 Z= 0.305 Chirality : 0.045 0.220 4827 Planarity : 0.005 0.063 5446 Dihedral : 4.608 23.052 4265 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.35 % Allowed : 8.78 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3964 helix: 1.63 (0.12), residues: 2090 sheet: -0.73 (0.21), residues: 596 loop : -1.49 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 430 HIS 0.008 0.001 HIS E 242 PHE 0.020 0.002 PHE B 542 TYR 0.023 0.001 TYR D 598 ARG 0.007 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 1583) hydrogen bonds : angle 4.00754 ( 4596) covalent geometry : bond 0.00404 (31358) covalent geometry : angle 0.57771 (42402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 557 time to evaluate : 3.321 Fit side-chains REVERT: A 470 ARG cc_start: 0.7763 (ttt-90) cc_final: 0.7476 (mtp180) REVERT: A 538 GLU cc_start: 0.7295 (tt0) cc_final: 0.6775 (mt-10) REVERT: A 571 VAL cc_start: 0.6404 (t) cc_final: 0.5901 (m) REVERT: A 611 GLU cc_start: 0.8429 (pm20) cc_final: 0.8002 (pm20) REVERT: A 645 MET cc_start: 0.8310 (mmm) cc_final: 0.7995 (mmt) REVERT: A 651 LYS cc_start: 0.7012 (mttm) cc_final: 0.6511 (mtpt) REVERT: A 653 LEU cc_start: 0.5496 (tp) cc_final: 0.5221 (tp) REVERT: A 809 GLU cc_start: 0.6567 (tt0) cc_final: 0.5974 (mt-10) REVERT: A 813 LYS cc_start: 0.6106 (mttt) cc_final: 0.5639 (mtmt) REVERT: B 41 LYS cc_start: 0.7910 (tttt) cc_final: 0.7694 (tttp) REVERT: B 60 MET cc_start: 0.8470 (ttm) cc_final: 0.8193 (ttm) REVERT: B 245 THR cc_start: 0.8332 (m) cc_final: 0.7686 (p) REVERT: B 270 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8007 (mtmm) REVERT: B 308 HIS cc_start: 0.6666 (t-90) cc_final: 0.6410 (t70) REVERT: B 312 ASN cc_start: 0.6758 (t0) cc_final: 0.6199 (m-40) REVERT: B 481 LYS cc_start: 0.6695 (tptm) cc_final: 0.6092 (tptt) REVERT: B 486 LYS cc_start: 0.6710 (mmtt) cc_final: 0.6199 (mmtm) REVERT: B 539 MET cc_start: 0.7005 (mtt) cc_final: 0.6425 (mmt) REVERT: B 592 LYS cc_start: 0.7701 (mttm) cc_final: 0.6827 (tptt) REVERT: B 663 THR cc_start: 0.8477 (m) cc_final: 0.8029 (p) REVERT: B 684 ARG cc_start: 0.7941 (tpt170) cc_final: 0.7528 (tpt90) REVERT: B 687 LYS cc_start: 0.7669 (tttt) cc_final: 0.6760 (tptp) REVERT: B 692 TYR cc_start: 0.8063 (m-80) cc_final: 0.7579 (m-10) REVERT: B 709 LYS cc_start: 0.6607 (mmtm) cc_final: 0.6095 (mmtp) REVERT: B 764 PRO cc_start: 0.8319 (Cg_endo) cc_final: 0.8002 (Cg_exo) REVERT: B 780 GLU cc_start: 0.6817 (mp0) cc_final: 0.6216 (tt0) REVERT: B 797 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7570 (mp0) REVERT: C 16 LYS cc_start: 0.6642 (mmtt) cc_final: 0.5925 (mtmt) REVERT: C 23 ARG cc_start: 0.7701 (ttp-170) cc_final: 0.7169 (ttp80) REVERT: C 53 MET cc_start: 0.8932 (mmm) cc_final: 0.8730 (ttt) REVERT: C 67 MET cc_start: 0.7945 (ptt) cc_final: 0.7430 (ptt) REVERT: C 103 PHE cc_start: 0.7893 (m-80) cc_final: 0.7643 (m-80) REVERT: C 191 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7622 (tpp80) REVERT: C 195 VAL cc_start: 0.8993 (m) cc_final: 0.8765 (t) REVERT: C 353 LYS cc_start: 0.7242 (ptpp) cc_final: 0.6506 (mmtm) REVERT: C 363 GLU cc_start: 0.7134 (tt0) cc_final: 0.6613 (mt-10) REVERT: C 364 ARG cc_start: 0.6611 (tpt-90) cc_final: 0.5395 (tpp-160) REVERT: C 625 ILE cc_start: 0.8427 (mt) cc_final: 0.8106 (pt) REVERT: C 627 TYR cc_start: 0.6655 (m-80) cc_final: 0.6112 (m-80) REVERT: C 638 MET cc_start: 0.8418 (tmm) cc_final: 0.8050 (ttt) REVERT: C 757 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8141 (mtt-85) REVERT: C 826 ASP cc_start: 0.7221 (t0) cc_final: 0.7019 (t70) REVERT: D 11 ILE cc_start: 0.7435 (mt) cc_final: 0.7203 (mm) REVERT: D 149 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7846 (ttm170) REVERT: D 228 ASP cc_start: 0.7915 (p0) cc_final: 0.7687 (p0) REVERT: D 269 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7309 (ttmt) REVERT: D 356 ASP cc_start: 0.6879 (m-30) cc_final: 0.6603 (m-30) REVERT: D 363 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 386 GLU cc_start: 0.7126 (pp20) cc_final: 0.6871 (pp20) REVERT: D 389 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7294 (mm110) REVERT: D 436 SER cc_start: 0.8673 (t) cc_final: 0.8396 (p) REVERT: D 574 MET cc_start: 0.8061 (mmt) cc_final: 0.7596 (tpt) REVERT: D 626 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7885 (mtmm) REVERT: D 836 GLU cc_start: 0.8087 (tt0) cc_final: 0.7634 (mm-30) REVERT: E 152 ASN cc_start: 0.6993 (m-40) cc_final: 0.6562 (m-40) REVERT: E 192 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7200 (mm-30) REVERT: E 282 GLU cc_start: 0.6610 (mp0) cc_final: 0.6182 (mt-10) REVERT: E 356 ASP cc_start: 0.7676 (m-30) cc_final: 0.7202 (m-30) REVERT: E 364 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7453 (ttt180) REVERT: E 470 ARG cc_start: 0.6556 (mtp-110) cc_final: 0.6019 (ttm170) REVERT: E 480 LEU cc_start: 0.6326 (mp) cc_final: 0.5988 (mt) REVERT: E 481 LYS cc_start: 0.5426 (ptmt) cc_final: 0.4950 (pptt) REVERT: E 576 MET cc_start: 0.8249 (mtm) cc_final: 0.7992 (mtm) REVERT: E 592 LYS cc_start: 0.7673 (mtmt) cc_final: 0.6933 (mttm) REVERT: E 676 ASP cc_start: 0.7224 (t0) cc_final: 0.6797 (t0) REVERT: E 757 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7188 (mtt-85) REVERT: E 863 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: F 520 PHE cc_start: 0.8049 (t80) cc_final: 0.7789 (t80) REVERT: F 533 LYS cc_start: 0.6561 (mmtp) cc_final: 0.6168 (mmmt) REVERT: F 556 MET cc_start: 0.7440 (mtt) cc_final: 0.7104 (mtt) REVERT: F 780 GLU cc_start: 0.6711 (pm20) cc_final: 0.6329 (pt0) outliers start: 44 outliers final: 35 residues processed: 581 average time/residue: 0.4217 time to fit residues: 388.3165 Evaluate side-chains 545 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 509 time to evaluate : 3.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 741 HIS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 828 LYS Chi-restraints excluded: chain E residue 856 MET Chi-restraints excluded: chain E residue 863 TYR Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 22 optimal weight: 1.9990 chunk 394 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 212 optimal weight: 0.0870 chunk 112 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 446 ASN C 850 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.141420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.113914 restraints weight = 36004.811| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.71 r_work: 0.2941 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 31358 Z= 0.227 Angle : 0.637 7.436 42402 Z= 0.337 Chirality : 0.047 0.217 4827 Planarity : 0.005 0.059 5446 Dihedral : 4.984 24.383 4265 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.86 % Allowed : 11.61 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 3964 helix: 1.37 (0.11), residues: 2089 sheet: -0.95 (0.20), residues: 596 loop : -1.58 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 430 HIS 0.010 0.002 HIS E 242 PHE 0.023 0.002 PHE E 371 TYR 0.034 0.002 TYR D 598 ARG 0.006 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.05990 ( 1583) hydrogen bonds : angle 4.08750 ( 4596) covalent geometry : bond 0.00560 (31358) covalent geometry : angle 0.63677 (42402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 523 time to evaluate : 3.645 Fit side-chains REVERT: A 499 ASN cc_start: 0.6673 (m-40) cc_final: 0.6419 (m-40) REVERT: A 538 GLU cc_start: 0.7430 (tt0) cc_final: 0.6915 (mt-10) REVERT: A 611 GLU cc_start: 0.8391 (pm20) cc_final: 0.7981 (pm20) REVERT: A 809 GLU cc_start: 0.6873 (tt0) cc_final: 0.6131 (mt-10) REVERT: A 813 LYS cc_start: 0.6135 (mttt) cc_final: 0.5661 (mtmt) REVERT: B 48 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8185 (mtp) REVERT: B 270 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8224 (mtmm) REVERT: B 308 HIS cc_start: 0.6709 (t-170) cc_final: 0.6397 (t70) REVERT: B 312 ASN cc_start: 0.7068 (t0) cc_final: 0.6385 (m110) REVERT: B 481 LYS cc_start: 0.6661 (tptm) cc_final: 0.6034 (tptt) REVERT: B 486 LYS cc_start: 0.6845 (mmtt) cc_final: 0.6629 (mmtm) REVERT: B 496 PHE cc_start: 0.5711 (t80) cc_final: 0.5211 (t80) REVERT: B 592 LYS cc_start: 0.7811 (mttm) cc_final: 0.6890 (tptt) REVERT: B 663 THR cc_start: 0.8465 (m) cc_final: 0.7926 (p) REVERT: B 687 LYS cc_start: 0.7648 (tttt) cc_final: 0.6644 (tptp) REVERT: B 709 LYS cc_start: 0.6687 (mmtm) cc_final: 0.6374 (mmtp) REVERT: B 780 GLU cc_start: 0.7013 (mp0) cc_final: 0.6461 (tt0) REVERT: C 16 LYS cc_start: 0.6695 (mmtt) cc_final: 0.5909 (mtmt) REVERT: C 23 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7099 (ttp80) REVERT: C 103 PHE cc_start: 0.8002 (m-80) cc_final: 0.7704 (m-80) REVERT: C 191 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7729 (tpp80) REVERT: C 195 VAL cc_start: 0.9129 (m) cc_final: 0.8907 (t) REVERT: C 266 LYS cc_start: 0.7140 (tptm) cc_final: 0.6841 (tppt) REVERT: C 353 LYS cc_start: 0.7146 (ptpp) cc_final: 0.6526 (mmtm) REVERT: C 363 GLU cc_start: 0.7326 (tt0) cc_final: 0.6717 (mt-10) REVERT: C 556 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7368 (mpp) REVERT: C 627 TYR cc_start: 0.6957 (m-80) cc_final: 0.6511 (m-80) REVERT: C 638 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8133 (ttt) REVERT: C 757 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.8203 (mtt-85) REVERT: C 808 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: C 832 ASP cc_start: 0.7311 (m-30) cc_final: 0.7053 (m-30) REVERT: D 149 ARG cc_start: 0.8126 (ttm170) cc_final: 0.7880 (ttm170) REVERT: D 228 ASP cc_start: 0.8043 (p0) cc_final: 0.7819 (p0) REVERT: D 269 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7248 (ttmt) REVERT: D 356 ASP cc_start: 0.7207 (m-30) cc_final: 0.6969 (m-30) REVERT: D 363 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7543 (tm-30) REVERT: D 389 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7407 (mm110) REVERT: D 402 VAL cc_start: 0.8947 (m) cc_final: 0.8651 (t) REVERT: D 574 MET cc_start: 0.8103 (mmt) cc_final: 0.7678 (tpt) REVERT: D 626 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7889 (mtmm) REVERT: D 836 GLU cc_start: 0.8214 (tt0) cc_final: 0.7713 (mm-30) REVERT: E 18 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: E 25 ARG cc_start: 0.7284 (mtt90) cc_final: 0.7004 (mtt-85) REVERT: E 192 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7226 (mm-30) REVERT: E 282 GLU cc_start: 0.6764 (mp0) cc_final: 0.6384 (mt-10) REVERT: E 418 LYS cc_start: 0.8359 (mmtm) cc_final: 0.7971 (mmtp) REVERT: E 470 ARG cc_start: 0.6554 (mtp-110) cc_final: 0.6294 (mtp85) REVERT: E 481 LYS cc_start: 0.5478 (ptmt) cc_final: 0.4949 (pttp) REVERT: E 521 PHE cc_start: 0.7488 (p90) cc_final: 0.6977 (p90) REVERT: E 592 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7008 (mttm) REVERT: E 757 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7206 (mtt-85) REVERT: E 773 TYR cc_start: 0.8799 (t80) cc_final: 0.7616 (t80) REVERT: E 801 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6975 (mm-30) REVERT: E 863 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: F 520 PHE cc_start: 0.8054 (t80) cc_final: 0.7788 (t80) REVERT: F 533 LYS cc_start: 0.6699 (mmtp) cc_final: 0.6306 (mmmt) REVERT: F 556 MET cc_start: 0.7650 (mtt) cc_final: 0.7379 (mtt) REVERT: F 780 GLU cc_start: 0.6751 (pm20) cc_final: 0.6549 (pt0) outliers start: 93 outliers final: 59 residues processed: 581 average time/residue: 0.4395 time to fit residues: 407.1907 Evaluate side-chains 569 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 504 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 741 HIS Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 556 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 595 GLN Chi-restraints excluded: chain D residue 610 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 646 MET Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 721 PHE Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 828 LYS Chi-restraints excluded: chain E residue 856 MET Chi-restraints excluded: chain E residue 863 TYR Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 678 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 271 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 387 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 373 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 152 ASN F 744 HIS F 748 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.142471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.115047 restraints weight = 36109.109| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.70 r_work: 0.2956 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 31358 Z= 0.189 Angle : 0.582 7.166 42402 Z= 0.309 Chirality : 0.045 0.216 4827 Planarity : 0.005 0.059 5446 Dihedral : 4.873 27.431 4265 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.07 % Allowed : 13.48 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3964 helix: 1.44 (0.11), residues: 2089 sheet: -1.02 (0.20), residues: 596 loop : -1.54 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 459 HIS 0.008 0.001 HIS E 242 PHE 0.021 0.002 PHE C 758 TYR 0.021 0.002 TYR D 598 ARG 0.007 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.05250 ( 1583) hydrogen bonds : angle 3.95062 ( 4596) covalent geometry : bond 0.00463 (31358) covalent geometry : angle 0.58212 (42402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 515 time to evaluate : 3.277 Fit side-chains revert: symmetry clash REVERT: A 499 ASN cc_start: 0.6705 (m-40) cc_final: 0.6340 (m-40) REVERT: A 538 GLU cc_start: 0.7414 (tt0) cc_final: 0.6895 (mt-10) REVERT: A 543 GLN cc_start: 0.8165 (tp40) cc_final: 0.7901 (mm-40) REVERT: A 611 GLU cc_start: 0.8379 (pm20) cc_final: 0.7953 (pm20) REVERT: A 809 GLU cc_start: 0.6878 (tt0) cc_final: 0.6234 (mt-10) REVERT: A 813 LYS cc_start: 0.6314 (mttt) cc_final: 0.5865 (mtmt) REVERT: B 18 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: B 40 ASP cc_start: 0.8481 (m-30) cc_final: 0.7929 (m-30) REVERT: B 48 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: B 308 HIS cc_start: 0.6627 (t-170) cc_final: 0.6304 (t70) REVERT: B 312 ASN cc_start: 0.7024 (t0) cc_final: 0.6369 (m110) REVERT: B 424 THR cc_start: 0.8364 (t) cc_final: 0.8076 (m) REVERT: B 481 LYS cc_start: 0.6585 (tptm) cc_final: 0.5990 (tptt) REVERT: B 486 LYS cc_start: 0.6762 (mmtt) cc_final: 0.6543 (mmtm) REVERT: B 592 LYS cc_start: 0.7840 (mttm) cc_final: 0.6864 (tptt) REVERT: B 663 THR cc_start: 0.8448 (m) cc_final: 0.7903 (p) REVERT: B 687 LYS cc_start: 0.7504 (tttt) cc_final: 0.6507 (tptp) REVERT: B 709 LYS cc_start: 0.6659 (mmtm) cc_final: 0.6354 (mmtp) REVERT: B 780 GLU cc_start: 0.6924 (mp0) cc_final: 0.6344 (tt0) REVERT: C 16 LYS cc_start: 0.6557 (mmtt) cc_final: 0.5847 (mtmt) REVERT: C 23 ARG cc_start: 0.7754 (ttp-170) cc_final: 0.7100 (ttp80) REVERT: C 103 PHE cc_start: 0.8040 (m-80) cc_final: 0.7754 (m-80) REVERT: C 191 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7717 (tpp80) REVERT: C 262 ASP cc_start: 0.7473 (m-30) cc_final: 0.7104 (m-30) REVERT: C 266 LYS cc_start: 0.7137 (tptm) cc_final: 0.6841 (tppt) REVERT: C 353 LYS cc_start: 0.7119 (ptpp) cc_final: 0.6421 (mmtm) REVERT: C 363 GLU cc_start: 0.7319 (tt0) cc_final: 0.6680 (mt-10) REVERT: C 556 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7381 (mpp) REVERT: C 627 TYR cc_start: 0.6978 (m-80) cc_final: 0.6546 (m-80) REVERT: C 638 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.6957 (tmm) REVERT: C 691 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7910 (tm-30) REVERT: C 757 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8199 (mtt-85) REVERT: C 808 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: C 832 ASP cc_start: 0.7239 (m-30) cc_final: 0.6999 (m-30) REVERT: D 269 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7249 (ttmt) REVERT: D 282 GLU cc_start: 0.5847 (tp30) cc_final: 0.5637 (tp30) REVERT: D 356 ASP cc_start: 0.7197 (m-30) cc_final: 0.6935 (m-30) REVERT: D 363 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7511 (tm-30) REVERT: D 389 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7432 (mm110) REVERT: D 574 MET cc_start: 0.8140 (mmt) cc_final: 0.7732 (tpt) REVERT: D 836 GLU cc_start: 0.8191 (tt0) cc_final: 0.7691 (mm-30) REVERT: E 25 ARG cc_start: 0.7231 (mtt90) cc_final: 0.6963 (mtt-85) REVERT: E 152 ASN cc_start: 0.7195 (m110) cc_final: 0.6768 (m-40) REVERT: E 192 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7190 (mm-30) REVERT: E 282 GLU cc_start: 0.6674 (mp0) cc_final: 0.6295 (mt-10) REVERT: E 418 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7929 (mmtp) REVERT: E 481 LYS cc_start: 0.5404 (ptmt) cc_final: 0.4929 (pttp) REVERT: E 521 PHE cc_start: 0.7546 (p90) cc_final: 0.7078 (p90) REVERT: E 592 LYS cc_start: 0.7703 (mtmt) cc_final: 0.6981 (mttm) REVERT: E 676 ASP cc_start: 0.7392 (t0) cc_final: 0.6971 (t0) REVERT: E 757 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7160 (mtt-85) REVERT: E 773 TYR cc_start: 0.8790 (t80) cc_final: 0.7660 (t80) REVERT: E 801 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6971 (mm-30) REVERT: E 863 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: F 478 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: F 520 PHE cc_start: 0.8069 (t80) cc_final: 0.7812 (t80) REVERT: F 533 LYS cc_start: 0.6692 (mmtp) cc_final: 0.6295 (mmmt) REVERT: F 556 MET cc_start: 0.7754 (mtt) cc_final: 0.7504 (mtt) REVERT: F 780 GLU cc_start: 0.6691 (pm20) cc_final: 0.6418 (pt0) REVERT: F 797 GLU cc_start: 0.4608 (OUTLIER) cc_final: 0.4020 (mt-10) outliers start: 100 outliers final: 63 residues processed: 576 average time/residue: 0.4424 time to fit residues: 408.5135 Evaluate side-chains 578 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 507 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 741 HIS Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 556 MET Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 721 PHE Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 595 GLN Chi-restraints excluded: chain D residue 610 SER Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 610 SER Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 730 HIS Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 828 LYS Chi-restraints excluded: chain E residue 856 MET Chi-restraints excluded: chain E residue 863 TYR Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 678 THR Chi-restraints excluded: chain F residue 797 GLU Chi-restraints excluded: chain F residue 807 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 201 optimal weight: 3.9990 chunk 374 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 379 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 377 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 330 optimal weight: 0.2980 chunk 352 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 ASN B 744 HIS B 748 ASN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN D 256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.145463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.119096 restraints weight = 35758.198| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.55 r_work: 0.3030 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31358 Z= 0.126 Angle : 0.508 6.728 42402 Z= 0.270 Chirality : 0.043 0.178 4827 Planarity : 0.004 0.055 5446 Dihedral : 4.534 24.652 4265 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.73 % Allowed : 14.52 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3964 helix: 1.72 (0.12), residues: 2091 sheet: -0.99 (0.20), residues: 596 loop : -1.43 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 459 HIS 0.004 0.001 HIS C 775 PHE 0.020 0.001 PHE A 721 TYR 0.022 0.001 TYR E 867 ARG 0.009 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1583) hydrogen bonds : angle 3.76194 ( 4596) covalent geometry : bond 0.00291 (31358) covalent geometry : angle 0.50841 (42402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 517 time to evaluate : 3.343 Fit side-chains REVERT: A 499 ASN cc_start: 0.6753 (m-40) cc_final: 0.6406 (m-40) REVERT: A 522 ASP cc_start: 0.7638 (t0) cc_final: 0.6816 (m-30) REVERT: A 538 GLU cc_start: 0.7314 (tt0) cc_final: 0.6772 (mt-10) REVERT: A 611 GLU cc_start: 0.8358 (pm20) cc_final: 0.7866 (pm20) REVERT: A 809 GLU cc_start: 0.6847 (tt0) cc_final: 0.6198 (mt-10) REVERT: A 813 LYS cc_start: 0.6431 (mttt) cc_final: 0.5957 (mtmt) REVERT: B 18 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: B 40 ASP cc_start: 0.8364 (m-30) cc_final: 0.7912 (m-30) REVERT: B 48 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8057 (mtp) REVERT: B 270 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8020 (mtmm) REVERT: B 308 HIS cc_start: 0.6622 (t-170) cc_final: 0.6365 (t70) REVERT: B 312 ASN cc_start: 0.6907 (t0) cc_final: 0.6337 (m-40) REVERT: B 481 LYS cc_start: 0.6470 (tptm) cc_final: 0.5912 (tptt) REVERT: B 486 LYS cc_start: 0.6697 (mmtt) cc_final: 0.6488 (mmtm) REVERT: B 592 LYS cc_start: 0.7780 (mttm) cc_final: 0.6799 (tptt) REVERT: B 684 ARG cc_start: 0.7911 (tpt170) cc_final: 0.7519 (tpt90) REVERT: B 687 LYS cc_start: 0.7467 (tttt) cc_final: 0.6429 (tptp) REVERT: B 709 LYS cc_start: 0.6617 (mmtm) cc_final: 0.6308 (mmtp) REVERT: B 780 GLU cc_start: 0.6790 (mp0) cc_final: 0.6226 (tt0) REVERT: C 16 LYS cc_start: 0.6426 (mmtt) cc_final: 0.5740 (mtmt) REVERT: C 23 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7007 (ttp80) REVERT: C 103 PHE cc_start: 0.7879 (m-80) cc_final: 0.7658 (m-80) REVERT: C 191 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7712 (tpp80) REVERT: C 266 LYS cc_start: 0.7020 (tptm) cc_final: 0.6732 (tppt) REVERT: C 353 LYS cc_start: 0.7125 (ptpp) cc_final: 0.6431 (mmtm) REVERT: C 363 GLU cc_start: 0.7200 (tt0) cc_final: 0.6559 (mt-10) REVERT: C 364 ARG cc_start: 0.6838 (tpp80) cc_final: 0.5521 (tpp-160) REVERT: C 556 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7155 (mpp) REVERT: C 627 TYR cc_start: 0.6846 (m-80) cc_final: 0.6385 (m-80) REVERT: C 691 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7766 (tm-30) REVERT: C 808 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: C 832 ASP cc_start: 0.7135 (m-30) cc_final: 0.6913 (m-30) REVERT: D 163 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: D 269 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7202 (ttmt) REVERT: D 356 ASP cc_start: 0.7064 (m-30) cc_final: 0.6811 (m-30) REVERT: D 363 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7468 (tm-30) REVERT: D 389 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7242 (mm110) REVERT: D 574 MET cc_start: 0.8088 (mmt) cc_final: 0.7711 (tpt) REVERT: D 836 GLU cc_start: 0.8053 (tt0) cc_final: 0.7544 (mm-30) REVERT: E 25 ARG cc_start: 0.7092 (mtt90) cc_final: 0.6810 (mtt-85) REVERT: E 152 ASN cc_start: 0.7072 (m110) cc_final: 0.6620 (m-40) REVERT: E 192 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7113 (mm-30) REVERT: E 418 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7767 (mmtp) REVERT: E 481 LYS cc_start: 0.5376 (ptmt) cc_final: 0.4890 (pttp) REVERT: E 521 PHE cc_start: 0.7510 (p90) cc_final: 0.7070 (p90) REVERT: E 592 LYS cc_start: 0.7684 (mtmt) cc_final: 0.6935 (mttm) REVERT: E 676 ASP cc_start: 0.7365 (t0) cc_final: 0.6846 (t0) REVERT: E 757 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7103 (mtt-85) REVERT: E 773 TYR cc_start: 0.8743 (t80) cc_final: 0.7640 (t80) REVERT: E 801 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6838 (tp30) REVERT: E 863 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: F 478 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: F 520 PHE cc_start: 0.8004 (t80) cc_final: 0.7710 (t80) REVERT: F 533 LYS cc_start: 0.6650 (mmtp) cc_final: 0.6242 (mmmt) REVERT: F 780 GLU cc_start: 0.6604 (pm20) cc_final: 0.6403 (pt0) REVERT: F 797 GLU cc_start: 0.4705 (OUTLIER) cc_final: 0.3924 (mp0) outliers start: 89 outliers final: 62 residues processed: 575 average time/residue: 0.4202 time to fit residues: 388.3060 Evaluate side-chains 571 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 501 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 741 HIS Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 556 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 721 PHE Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 595 GLN Chi-restraints excluded: chain D residue 610 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 610 SER Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 730 HIS Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 828 LYS Chi-restraints excluded: chain E residue 837 MET Chi-restraints excluded: chain E residue 863 TYR Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 679 ASP Chi-restraints excluded: chain F residue 797 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 263 optimal weight: 4.9990 chunk 317 optimal weight: 2.9990 chunk 374 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN C 857 ASN ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 ASN D 340 HIS ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.141722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.114983 restraints weight = 36258.786| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.52 r_work: 0.2973 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31358 Z= 0.208 Angle : 0.602 7.068 42402 Z= 0.318 Chirality : 0.046 0.200 4827 Planarity : 0.005 0.058 5446 Dihedral : 4.878 25.232 4265 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.47 % Allowed : 15.29 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3964 helix: 1.51 (0.12), residues: 2090 sheet: -1.07 (0.20), residues: 596 loop : -1.49 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 430 HIS 0.008 0.001 HIS E 242 PHE 0.022 0.002 PHE C 758 TYR 0.021 0.002 TYR D 598 ARG 0.007 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.05518 ( 1583) hydrogen bonds : angle 3.92947 ( 4596) covalent geometry : bond 0.00513 (31358) covalent geometry : angle 0.60155 (42402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 503 time to evaluate : 3.613 Fit side-chains REVERT: A 499 ASN cc_start: 0.6687 (m-40) cc_final: 0.6318 (m-40) REVERT: A 538 GLU cc_start: 0.7322 (tt0) cc_final: 0.6800 (mt-10) REVERT: A 611 GLU cc_start: 0.8394 (pm20) cc_final: 0.7959 (pm20) REVERT: A 809 GLU cc_start: 0.7025 (tt0) cc_final: 0.6475 (mt-10) REVERT: B 18 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: B 40 ASP cc_start: 0.8456 (m-30) cc_final: 0.7907 (m-30) REVERT: B 48 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8057 (mtp) REVERT: B 308 HIS cc_start: 0.6614 (t-170) cc_final: 0.6292 (t70) REVERT: B 312 ASN cc_start: 0.7055 (t0) cc_final: 0.6341 (m110) REVERT: B 424 THR cc_start: 0.8423 (t) cc_final: 0.8162 (m) REVERT: B 481 LYS cc_start: 0.6455 (tptm) cc_final: 0.5895 (tptt) REVERT: B 486 LYS cc_start: 0.6794 (mmtt) cc_final: 0.6519 (mmtm) REVERT: B 592 LYS cc_start: 0.7815 (mttm) cc_final: 0.6867 (tptt) REVERT: B 663 THR cc_start: 0.8416 (m) cc_final: 0.7862 (p) REVERT: B 687 LYS cc_start: 0.7507 (tttt) cc_final: 0.6507 (tptp) REVERT: B 709 LYS cc_start: 0.6664 (mmtm) cc_final: 0.6185 (mmtp) REVERT: B 780 GLU cc_start: 0.6872 (mp0) cc_final: 0.6328 (tt0) REVERT: C 16 LYS cc_start: 0.6598 (mmtt) cc_final: 0.5872 (mtmt) REVERT: C 23 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7145 (ttp80) REVERT: C 103 PHE cc_start: 0.8048 (m-80) cc_final: 0.7778 (m-80) REVERT: C 191 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7777 (tpp80) REVERT: C 266 LYS cc_start: 0.7139 (tptm) cc_final: 0.6821 (tppt) REVERT: C 353 LYS cc_start: 0.7153 (ptpp) cc_final: 0.6557 (mmtm) REVERT: C 363 GLU cc_start: 0.7264 (tt0) cc_final: 0.6628 (mt-10) REVERT: C 364 ARG cc_start: 0.6790 (tpp80) cc_final: 0.5555 (tpp-160) REVERT: C 556 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: C 627 TYR cc_start: 0.6997 (m-80) cc_final: 0.6572 (m-80) REVERT: C 629 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7888 (pp) REVERT: C 638 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8161 (ttt) REVERT: C 757 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8179 (mtt-85) REVERT: C 808 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: C 832 ASP cc_start: 0.7201 (m-30) cc_final: 0.6978 (m-30) REVERT: D 163 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: D 228 ASP cc_start: 0.7827 (p0) cc_final: 0.7545 (p0) REVERT: D 269 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7286 (ttmt) REVERT: D 328 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7306 (mm-30) REVERT: D 356 ASP cc_start: 0.7176 (m-30) cc_final: 0.6887 (m-30) REVERT: D 363 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7495 (tm-30) REVERT: D 389 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7346 (mm110) REVERT: D 574 MET cc_start: 0.8075 (mmt) cc_final: 0.7691 (tpt) REVERT: D 598 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: D 836 GLU cc_start: 0.8129 (tt0) cc_final: 0.7608 (mm-30) REVERT: E 25 ARG cc_start: 0.7191 (mtt90) cc_final: 0.6915 (mtt-85) REVERT: E 192 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7144 (mm-30) REVERT: E 282 GLU cc_start: 0.6695 (mp0) cc_final: 0.6339 (mt-10) REVERT: E 418 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7891 (mmtp) REVERT: E 481 LYS cc_start: 0.5322 (ptmt) cc_final: 0.4879 (pttp) REVERT: E 521 PHE cc_start: 0.7530 (p90) cc_final: 0.7118 (p90) REVERT: E 592 LYS cc_start: 0.7670 (mtmt) cc_final: 0.6933 (mttm) REVERT: E 676 ASP cc_start: 0.7580 (t0) cc_final: 0.6943 (t0) REVERT: E 757 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7121 (mtt-85) REVERT: E 801 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6929 (tp30) REVERT: E 863 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: F 533 LYS cc_start: 0.6706 (mmtp) cc_final: 0.6299 (mmmt) REVERT: F 780 GLU cc_start: 0.6731 (pm20) cc_final: 0.6488 (pt0) REVERT: F 797 GLU cc_start: 0.4834 (OUTLIER) cc_final: 0.4360 (mt-10) outliers start: 113 outliers final: 79 residues processed: 578 average time/residue: 0.4642 time to fit residues: 434.3325 Evaluate side-chains 585 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 496 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 741 HIS Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 487 LYS Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 556 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 721 PHE Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 595 GLN Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 610 SER Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 635 LEU Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 721 PHE Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 828 LYS Chi-restraints excluded: chain E residue 837 MET Chi-restraints excluded: chain E residue 863 TYR Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 678 THR Chi-restraints excluded: chain F residue 797 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 365 optimal weight: 0.0050 chunk 54 optimal weight: 9.9990 chunk 230 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 317 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 GLN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 857 ASN ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.147305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.119787 restraints weight = 35878.100| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.60 r_work: 0.3029 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31358 Z= 0.104 Angle : 0.485 6.506 42402 Z= 0.258 Chirality : 0.042 0.161 4827 Planarity : 0.004 0.054 5446 Dihedral : 4.383 22.494 4265 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.43 % Allowed : 16.61 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3964 helix: 1.88 (0.12), residues: 2091 sheet: -0.97 (0.20), residues: 596 loop : -1.35 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 459 HIS 0.004 0.001 HIS C 730 PHE 0.023 0.001 PHE A 721 TYR 0.018 0.001 TYR F 669 ARG 0.010 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1583) hydrogen bonds : angle 3.67588 ( 4596) covalent geometry : bond 0.00223 (31358) covalent geometry : angle 0.48513 (42402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 526 time to evaluate : 3.409 Fit side-chains REVERT: A 499 ASN cc_start: 0.6705 (m-40) cc_final: 0.6324 (m-40) REVERT: A 522 ASP cc_start: 0.7735 (t0) cc_final: 0.6921 (m-30) REVERT: A 538 GLU cc_start: 0.7273 (tt0) cc_final: 0.6753 (mt-10) REVERT: A 611 GLU cc_start: 0.8395 (pm20) cc_final: 0.7868 (pm20) REVERT: A 809 GLU cc_start: 0.6799 (tt0) cc_final: 0.6229 (mt-10) REVERT: B 18 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: B 48 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8061 (ttp) REVERT: B 308 HIS cc_start: 0.6645 (t-170) cc_final: 0.6389 (t70) REVERT: B 312 ASN cc_start: 0.6910 (t0) cc_final: 0.6276 (m-40) REVERT: B 481 LYS cc_start: 0.6457 (tptm) cc_final: 0.5886 (tptt) REVERT: B 486 LYS cc_start: 0.6567 (mmtt) cc_final: 0.6299 (mmtm) REVERT: B 592 LYS cc_start: 0.7773 (mttm) cc_final: 0.6812 (tptt) REVERT: B 638 MET cc_start: 0.8010 (ttt) cc_final: 0.7636 (ttt) REVERT: B 684 ARG cc_start: 0.7917 (tpt170) cc_final: 0.7523 (tpt90) REVERT: B 687 LYS cc_start: 0.7559 (tttt) cc_final: 0.6556 (tptp) REVERT: B 709 LYS cc_start: 0.6661 (mmtm) cc_final: 0.6357 (mmtp) REVERT: B 780 GLU cc_start: 0.6824 (mp0) cc_final: 0.6251 (tt0) REVERT: B 829 GLU cc_start: 0.5991 (tt0) cc_final: 0.5408 (tp30) REVERT: C 16 LYS cc_start: 0.6400 (mmtt) cc_final: 0.5717 (mtmt) REVERT: C 23 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7096 (ttp80) REVERT: C 191 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7830 (tpp80) REVERT: C 266 LYS cc_start: 0.7038 (tptm) cc_final: 0.6724 (tppt) REVERT: C 353 LYS cc_start: 0.7156 (ptpp) cc_final: 0.6539 (mmtm) REVERT: C 363 GLU cc_start: 0.7283 (tt0) cc_final: 0.6660 (mt-10) REVERT: C 364 ARG cc_start: 0.6849 (tpp80) cc_final: 0.5597 (tpp-160) REVERT: C 625 ILE cc_start: 0.8315 (mt) cc_final: 0.8062 (pt) REVERT: C 627 TYR cc_start: 0.6944 (m-80) cc_final: 0.6367 (m-80) REVERT: C 808 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: D 11 ILE cc_start: 0.7859 (mt) cc_final: 0.7566 (mm) REVERT: D 163 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: D 174 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7242 (mt) REVERT: D 269 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7276 (ttmt) REVERT: D 328 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7149 (mm-30) REVERT: D 356 ASP cc_start: 0.7112 (m-30) cc_final: 0.6852 (m-30) REVERT: D 363 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7573 (tm-30) REVERT: D 574 MET cc_start: 0.8127 (mmt) cc_final: 0.7770 (tpt) REVERT: D 667 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8533 (mt-10) REVERT: D 836 GLU cc_start: 0.8149 (tt0) cc_final: 0.7640 (mm-30) REVERT: E 25 ARG cc_start: 0.7164 (mtt90) cc_final: 0.6895 (mtt-85) REVERT: E 152 ASN cc_start: 0.7092 (m110) cc_final: 0.6653 (m-40) REVERT: E 192 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6946 (mt-10) REVERT: E 418 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7799 (mmtp) REVERT: E 481 LYS cc_start: 0.5390 (ptmt) cc_final: 0.4916 (pttp) REVERT: E 521 PHE cc_start: 0.7516 (p90) cc_final: 0.7073 (p90) REVERT: E 592 LYS cc_start: 0.7630 (mtmt) cc_final: 0.6884 (mttm) REVERT: E 676 ASP cc_start: 0.7605 (t0) cc_final: 0.6787 (t0) REVERT: E 757 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7261 (mtt-85) REVERT: E 801 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6935 (tp30) REVERT: F 533 LYS cc_start: 0.6670 (mmtp) cc_final: 0.6277 (mmmt) REVERT: F 780 GLU cc_start: 0.6809 (pm20) cc_final: 0.6534 (pt0) REVERT: F 797 GLU cc_start: 0.4837 (OUTLIER) cc_final: 0.4230 (mt-10) outliers start: 79 outliers final: 62 residues processed: 578 average time/residue: 0.4139 time to fit residues: 382.8560 Evaluate side-chains 568 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 500 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 721 PHE Chi-restraints excluded: chain B residue 741 HIS Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 593 MET Chi-restraints excluded: chain C residue 721 PHE Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 784 GLU Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 730 HIS Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 828 LYS Chi-restraints excluded: chain E residue 837 MET Chi-restraints excluded: chain E residue 863 TYR Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 678 THR Chi-restraints excluded: chain F residue 787 ASP Chi-restraints excluded: chain F residue 797 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 191 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 338 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 341 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.145539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.118323 restraints weight = 36011.160| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.68 r_work: 0.2998 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31358 Z= 0.133 Angle : 0.519 6.456 42402 Z= 0.275 Chirality : 0.043 0.191 4827 Planarity : 0.004 0.052 5446 Dihedral : 4.441 22.020 4265 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.64 % Allowed : 16.55 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3964 helix: 1.86 (0.12), residues: 2090 sheet: -0.98 (0.20), residues: 596 loop : -1.35 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 459 HIS 0.005 0.001 HIS E 242 PHE 0.022 0.001 PHE A 721 TYR 0.013 0.001 TYR F 669 ARG 0.009 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 1583) hydrogen bonds : angle 3.71506 ( 4596) covalent geometry : bond 0.00312 (31358) covalent geometry : angle 0.51908 (42402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 506 time to evaluate : 3.528 Fit side-chains revert: symmetry clash REVERT: A 499 ASN cc_start: 0.6710 (m-40) cc_final: 0.6359 (m-40) REVERT: A 538 GLU cc_start: 0.7293 (tt0) cc_final: 0.6785 (mt-10) REVERT: A 611 GLU cc_start: 0.8421 (pm20) cc_final: 0.7927 (pm20) REVERT: A 809 GLU cc_start: 0.6822 (tt0) cc_final: 0.6265 (mt-10) REVERT: B 18 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: B 48 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8118 (mtp) REVERT: B 308 HIS cc_start: 0.6650 (t-170) cc_final: 0.6402 (t70) REVERT: B 312 ASN cc_start: 0.6876 (t0) cc_final: 0.6296 (m-40) REVERT: B 481 LYS cc_start: 0.6386 (tptm) cc_final: 0.5817 (tptt) REVERT: B 486 LYS cc_start: 0.6684 (mmtt) cc_final: 0.6420 (mmtm) REVERT: B 592 LYS cc_start: 0.7775 (mttm) cc_final: 0.6840 (tptt) REVERT: B 684 ARG cc_start: 0.7935 (tpt170) cc_final: 0.7542 (tpt90) REVERT: B 687 LYS cc_start: 0.7556 (tttt) cc_final: 0.6548 (tptp) REVERT: B 709 LYS cc_start: 0.6653 (mmtm) cc_final: 0.6344 (mmtp) REVERT: B 780 GLU cc_start: 0.6880 (mp0) cc_final: 0.6302 (tt0) REVERT: B 829 GLU cc_start: 0.5873 (tt0) cc_final: 0.5312 (tp30) REVERT: C 16 LYS cc_start: 0.6466 (mmtt) cc_final: 0.5771 (mtmt) REVERT: C 23 ARG cc_start: 0.7755 (ttp-170) cc_final: 0.7109 (ttp80) REVERT: C 191 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7823 (tpp80) REVERT: C 266 LYS cc_start: 0.7088 (tptm) cc_final: 0.6781 (tppt) REVERT: C 353 LYS cc_start: 0.7158 (ptpp) cc_final: 0.6539 (mmtm) REVERT: C 363 GLU cc_start: 0.7280 (tt0) cc_final: 0.6657 (mt-10) REVERT: C 364 ARG cc_start: 0.6806 (tpp80) cc_final: 0.5581 (tpp-160) REVERT: C 482 ASN cc_start: 0.7600 (m-40) cc_final: 0.7375 (m110) REVERT: C 627 TYR cc_start: 0.6998 (m-80) cc_final: 0.6409 (m-80) REVERT: C 638 MET cc_start: 0.8362 (tmm) cc_final: 0.7875 (ttt) REVERT: C 808 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: D 163 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: D 228 ASP cc_start: 0.7748 (p0) cc_final: 0.7449 (p0) REVERT: D 269 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7279 (ttmt) REVERT: D 328 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7218 (mm-30) REVERT: D 356 ASP cc_start: 0.7169 (m-30) cc_final: 0.6909 (m-30) REVERT: D 363 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 389 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7371 (mm110) REVERT: D 574 MET cc_start: 0.8118 (mmt) cc_final: 0.7753 (tpt) REVERT: D 667 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8600 (mt-10) REVERT: D 836 GLU cc_start: 0.8157 (tt0) cc_final: 0.7654 (mm-30) REVERT: E 25 ARG cc_start: 0.7161 (mtt90) cc_final: 0.6892 (mtt-85) REVERT: E 152 ASN cc_start: 0.7095 (m110) cc_final: 0.6649 (m-40) REVERT: E 192 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6952 (mt-10) REVERT: E 282 GLU cc_start: 0.6624 (mp0) cc_final: 0.6156 (mt-10) REVERT: E 356 ASP cc_start: 0.7210 (m-30) cc_final: 0.6873 (m-30) REVERT: E 418 LYS cc_start: 0.8268 (mmtm) cc_final: 0.8066 (mmtt) REVERT: E 481 LYS cc_start: 0.5352 (ptmt) cc_final: 0.4874 (pttp) REVERT: E 521 PHE cc_start: 0.7527 (p90) cc_final: 0.7077 (p90) REVERT: E 592 LYS cc_start: 0.7649 (mtmt) cc_final: 0.6910 (mttm) REVERT: E 757 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7260 (mtt-85) REVERT: E 801 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6974 (tp30) REVERT: E 863 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: F 520 PHE cc_start: 0.8033 (t80) cc_final: 0.7783 (t80) REVERT: F 533 LYS cc_start: 0.6679 (mmtp) cc_final: 0.6286 (mmmt) REVERT: F 780 GLU cc_start: 0.6715 (pm20) cc_final: 0.6438 (pt0) outliers start: 86 outliers final: 67 residues processed: 564 average time/residue: 0.4205 time to fit residues: 380.1082 Evaluate side-chains 571 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 499 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 721 PHE Chi-restraints excluded: chain B residue 741 HIS Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 721 PHE Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 784 GLU Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 595 GLN Chi-restraints excluded: chain D residue 610 SER Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 730 HIS Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 828 LYS Chi-restraints excluded: chain E residue 837 MET Chi-restraints excluded: chain E residue 863 TYR Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 678 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 163 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 219 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 HIS E 748 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.145119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.117672 restraints weight = 35765.239| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.66 r_work: 0.2994 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31358 Z= 0.139 Angle : 0.528 6.544 42402 Z= 0.279 Chirality : 0.043 0.181 4827 Planarity : 0.004 0.052 5446 Dihedral : 4.503 21.893 4265 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.70 % Allowed : 16.46 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3964 helix: 1.84 (0.12), residues: 2086 sheet: -0.99 (0.20), residues: 596 loop : -1.37 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 459 HIS 0.005 0.001 HIS E 242 PHE 0.022 0.002 PHE A 721 TYR 0.014 0.001 TYR D 598 ARG 0.009 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 1583) hydrogen bonds : angle 3.73598 ( 4596) covalent geometry : bond 0.00328 (31358) covalent geometry : angle 0.52846 (42402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 505 time to evaluate : 3.816 Fit side-chains REVERT: A 499 ASN cc_start: 0.6779 (m-40) cc_final: 0.6420 (m-40) REVERT: A 522 ASP cc_start: 0.7733 (t0) cc_final: 0.6954 (m-30) REVERT: A 538 GLU cc_start: 0.7417 (tt0) cc_final: 0.6881 (mt-10) REVERT: A 611 GLU cc_start: 0.8422 (pm20) cc_final: 0.7929 (pm20) REVERT: A 809 GLU cc_start: 0.6851 (tt0) cc_final: 0.6290 (mt-10) REVERT: B 18 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: B 40 ASP cc_start: 0.8465 (m-30) cc_final: 0.8015 (m-30) REVERT: B 48 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8121 (mtp) REVERT: B 308 HIS cc_start: 0.6647 (t-170) cc_final: 0.6310 (t70) REVERT: B 312 ASN cc_start: 0.6947 (t0) cc_final: 0.6247 (m110) REVERT: B 424 THR cc_start: 0.8245 (t) cc_final: 0.7930 (m) REVERT: B 481 LYS cc_start: 0.6397 (tptm) cc_final: 0.5836 (tptt) REVERT: B 486 LYS cc_start: 0.6650 (mmtt) cc_final: 0.6409 (mmtm) REVERT: B 592 LYS cc_start: 0.7777 (mttm) cc_final: 0.6849 (tptt) REVERT: B 684 ARG cc_start: 0.7948 (tpt170) cc_final: 0.7554 (tpt90) REVERT: B 687 LYS cc_start: 0.7554 (tttt) cc_final: 0.6561 (tptp) REVERT: B 709 LYS cc_start: 0.6668 (mmtm) cc_final: 0.6366 (mmtp) REVERT: B 780 GLU cc_start: 0.6857 (mp0) cc_final: 0.6303 (tt0) REVERT: B 829 GLU cc_start: 0.5929 (tt0) cc_final: 0.5363 (tp30) REVERT: C 16 LYS cc_start: 0.6437 (mmtt) cc_final: 0.5744 (mtmt) REVERT: C 23 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7135 (ttp80) REVERT: C 191 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7834 (tpp80) REVERT: C 266 LYS cc_start: 0.7105 (tptm) cc_final: 0.6803 (tppt) REVERT: C 353 LYS cc_start: 0.7155 (ptpp) cc_final: 0.6550 (mmtm) REVERT: C 363 GLU cc_start: 0.7255 (tt0) cc_final: 0.6642 (mt-10) REVERT: C 364 ARG cc_start: 0.6806 (tpp80) cc_final: 0.5535 (tpp-160) REVERT: C 482 ASN cc_start: 0.7631 (m-40) cc_final: 0.7410 (m110) REVERT: C 556 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7187 (mpp) REVERT: C 808 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: D 163 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: D 228 ASP cc_start: 0.7765 (p0) cc_final: 0.7466 (p0) REVERT: D 269 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7317 (ttmt) REVERT: D 328 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7239 (mm-30) REVERT: D 356 ASP cc_start: 0.7197 (m-30) cc_final: 0.6925 (m-30) REVERT: D 363 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7571 (tm-30) REVERT: D 389 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7400 (mm110) REVERT: D 480 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8808 (mp) REVERT: D 574 MET cc_start: 0.8126 (mmt) cc_final: 0.7767 (tpt) REVERT: D 667 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8555 (mt-10) REVERT: D 836 GLU cc_start: 0.8159 (tt0) cc_final: 0.7666 (mm-30) REVERT: E 25 ARG cc_start: 0.7188 (mtt90) cc_final: 0.6913 (mtt-85) REVERT: E 152 ASN cc_start: 0.7090 (m110) cc_final: 0.6636 (m-40) REVERT: E 192 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7119 (mm-30) REVERT: E 282 GLU cc_start: 0.6683 (mp0) cc_final: 0.6223 (mt-10) REVERT: E 418 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7854 (mmtp) REVERT: E 481 LYS cc_start: 0.5446 (ptmt) cc_final: 0.4984 (pttp) REVERT: E 521 PHE cc_start: 0.7512 (p90) cc_final: 0.7085 (p90) REVERT: E 757 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7271 (mtt-85) REVERT: E 801 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6977 (tp30) REVERT: F 520 PHE cc_start: 0.8015 (t80) cc_final: 0.7767 (t80) REVERT: F 533 LYS cc_start: 0.6683 (mmtp) cc_final: 0.6304 (mmmt) REVERT: F 780 GLU cc_start: 0.6696 (pm20) cc_final: 0.6409 (pt0) outliers start: 88 outliers final: 72 residues processed: 563 average time/residue: 0.4367 time to fit residues: 396.8039 Evaluate side-chains 579 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 501 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 721 PHE Chi-restraints excluded: chain B residue 741 HIS Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 556 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 721 PHE Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 784 GLU Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 595 GLN Chi-restraints excluded: chain D residue 610 SER Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 730 HIS Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 828 LYS Chi-restraints excluded: chain E residue 837 MET Chi-restraints excluded: chain E residue 863 TYR Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 678 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 178 optimal weight: 7.9990 chunk 302 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 285 optimal weight: 0.8980 chunk 373 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 347 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 748 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.143806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.116299 restraints weight = 36075.273| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.64 r_work: 0.2978 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31358 Z= 0.165 Angle : 0.562 7.763 42402 Z= 0.298 Chirality : 0.044 0.191 4827 Planarity : 0.005 0.053 5446 Dihedral : 4.643 23.002 4265 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.67 % Allowed : 16.83 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3964 helix: 1.72 (0.12), residues: 2092 sheet: -1.02 (0.20), residues: 596 loop : -1.41 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 459 HIS 0.006 0.001 HIS E 242 PHE 0.022 0.002 PHE A 721 TYR 0.019 0.001 TYR D 598 ARG 0.008 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 1583) hydrogen bonds : angle 3.82022 ( 4596) covalent geometry : bond 0.00398 (31358) covalent geometry : angle 0.56237 (42402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7928 Ramachandran restraints generated. 3964 Oldfield, 0 Emsley, 3964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 488 time to evaluate : 3.481 Fit side-chains REVERT: A 499 ASN cc_start: 0.6762 (m-40) cc_final: 0.6412 (m-40) REVERT: A 522 ASP cc_start: 0.7743 (t0) cc_final: 0.6965 (m-30) REVERT: A 538 GLU cc_start: 0.7360 (tt0) cc_final: 0.6878 (mt-10) REVERT: A 611 GLU cc_start: 0.8419 (pm20) cc_final: 0.7937 (pm20) REVERT: A 809 GLU cc_start: 0.7039 (tt0) cc_final: 0.6465 (mt-10) REVERT: B 18 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: B 40 ASP cc_start: 0.8482 (m-30) cc_final: 0.8003 (m-30) REVERT: B 48 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8055 (mtp) REVERT: B 308 HIS cc_start: 0.6629 (t-170) cc_final: 0.6307 (t70) REVERT: B 312 ASN cc_start: 0.6995 (t0) cc_final: 0.6305 (m110) REVERT: B 481 LYS cc_start: 0.6376 (tptm) cc_final: 0.5810 (tptt) REVERT: B 592 LYS cc_start: 0.7794 (mttm) cc_final: 0.6897 (tptt) REVERT: B 638 MET cc_start: 0.8090 (ttt) cc_final: 0.7736 (ttt) REVERT: B 663 THR cc_start: 0.8427 (m) cc_final: 0.7873 (p) REVERT: B 687 LYS cc_start: 0.7505 (tttt) cc_final: 0.6520 (tptp) REVERT: B 709 LYS cc_start: 0.6697 (mmtm) cc_final: 0.6377 (mmtp) REVERT: B 780 GLU cc_start: 0.6875 (mp0) cc_final: 0.6322 (tt0) REVERT: B 829 GLU cc_start: 0.5937 (tt0) cc_final: 0.5369 (tp30) REVERT: C 16 LYS cc_start: 0.6448 (mmtt) cc_final: 0.5749 (mtmt) REVERT: C 23 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7138 (ttp80) REVERT: C 191 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7827 (tpp80) REVERT: C 266 LYS cc_start: 0.7137 (tptm) cc_final: 0.6828 (tppt) REVERT: C 353 LYS cc_start: 0.7135 (ptpp) cc_final: 0.6549 (mmtm) REVERT: C 363 GLU cc_start: 0.7265 (tt0) cc_final: 0.6658 (mt-10) REVERT: C 364 ARG cc_start: 0.6842 (tpp80) cc_final: 0.5581 (tpp-160) REVERT: C 556 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7212 (mpp) REVERT: C 627 TYR cc_start: 0.6588 (m-80) cc_final: 0.6339 (m-80) REVERT: C 638 MET cc_start: 0.8400 (tmm) cc_final: 0.7973 (ttt) REVERT: C 808 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: D 163 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: D 228 ASP cc_start: 0.7794 (p0) cc_final: 0.7530 (p0) REVERT: D 269 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7325 (ttmt) REVERT: D 328 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7273 (mm-30) REVERT: D 356 ASP cc_start: 0.7212 (m-30) cc_final: 0.6922 (m-30) REVERT: D 363 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7585 (tm-30) REVERT: D 389 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7407 (mm110) REVERT: D 480 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8804 (mp) REVERT: D 574 MET cc_start: 0.8101 (mmt) cc_final: 0.7738 (tpt) REVERT: D 598 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: D 836 GLU cc_start: 0.8180 (tt0) cc_final: 0.7687 (mm-30) REVERT: E 25 ARG cc_start: 0.7238 (mtt90) cc_final: 0.6952 (mtt-85) REVERT: E 152 ASN cc_start: 0.7122 (m110) cc_final: 0.6680 (m-40) REVERT: E 192 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7153 (mm-30) REVERT: E 282 GLU cc_start: 0.6727 (mp0) cc_final: 0.6272 (mt-10) REVERT: E 418 LYS cc_start: 0.8282 (mmtm) cc_final: 0.7897 (mmtp) REVERT: E 481 LYS cc_start: 0.5452 (ptmt) cc_final: 0.4983 (pttp) REVERT: E 521 PHE cc_start: 0.7508 (p90) cc_final: 0.7120 (p90) REVERT: E 757 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7175 (mtt-85) REVERT: E 801 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6981 (tp30) REVERT: E 863 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: F 533 LYS cc_start: 0.6718 (mmtp) cc_final: 0.6297 (mmmt) REVERT: F 565 MET cc_start: 0.7783 (mtt) cc_final: 0.7281 (mtt) REVERT: F 780 GLU cc_start: 0.6700 (pm20) cc_final: 0.6390 (pt0) outliers start: 87 outliers final: 73 residues processed: 548 average time/residue: 0.4290 time to fit residues: 377.3336 Evaluate side-chains 567 residues out of total 3257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 486 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 741 HIS Chi-restraints excluded: chain B residue 767 MET Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 556 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 721 PHE Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 785 ILE Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 595 GLN Chi-restraints excluded: chain D residue 598 TYR Chi-restraints excluded: chain D residue 610 SER Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 825 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 721 PHE Chi-restraints excluded: chain E residue 730 HIS Chi-restraints excluded: chain E residue 746 VAL Chi-restraints excluded: chain E residue 767 MET Chi-restraints excluded: chain E residue 828 LYS Chi-restraints excluded: chain E residue 837 MET Chi-restraints excluded: chain E residue 863 TYR Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain F residue 484 MET Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 629 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 678 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 376 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 358 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 289 optimal weight: 0.0870 chunk 185 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 142 optimal weight: 0.0970 chunk 182 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN C 482 ASN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.149046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.122064 restraints weight = 35546.327| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.56 r_work: 0.3071 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31358 Z= 0.097 Angle : 0.479 6.234 42402 Z= 0.254 Chirality : 0.042 0.178 4827 Planarity : 0.004 0.050 5446 Dihedral : 4.217 20.345 4265 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.00 % Allowed : 17.68 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3964 helix: 1.99 (0.12), residues: 2092 sheet: -0.92 (0.20), residues: 608 loop : -1.31 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 459 HIS 0.003 0.001 HIS C 730 PHE 0.023 0.001 PHE A 721 TYR 0.015 0.001 TYR F 669 ARG 0.009 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 1583) hydrogen bonds : angle 3.64385 ( 4596) covalent geometry : bond 0.00207 (31358) covalent geometry : angle 0.47853 (42402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18208.82 seconds wall clock time: 315 minutes 9.00 seconds (18909.00 seconds total)